[gmx-users] doing restarts

[Juliette N.]

On 10 September 2011 18:03, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Juliette N. wrote:
>
>> Hello,
>>
>> I am trying to extend a simulation to 2 ns and wanted to know if I am
>> using the proper tools for this purpose. (version 4.5.4)
>>
>> 1) tpbconv –f old.trr -s old.tpr –e old.edr -o old-extend.tpr -until 2000
>>
>> mdrun -s old-extend.tpr  -cpi old.cpt   -o old-extend  -c old-extend -e
>> old-extend
>>
>> Is what I am doing correct?
>>
>>
> Yes.  Save yourself some typing with:
>
> mdrun -deffnm old-extend -cpi old.cpt
>
>
>  2) Can I use the following in 4.5.4 instead of above?
>>
>> mdrun -s old.tpr -cpi old.cpt -append 2000
>>
>>
> No.  The mdrun -append option does not take an argument; it is a boolean
> (i.e. -append/-noappend) to indicate whether old files are to be appended to
> or not.
>

Thank you. Where can I define how long simulation is going to be? I think
the advantage of append is that it combines old and old-extend energy files
and there is no need for

eneconv -f old-extend.edr  old.edr -o concatenate2ns.edr

Is that right?

I am just trying to get the most of the tools and skip unnecessary tools
like eneconv as far as it is possible.I am a little confused as there are
different ways explained on "doing restarts" page.

tpbconv –f old.trr -s old.tpr –e old.edr -o old-extend.tpr -until 2000

mdrun -deffnm old-extend -cpi old.cpt

does this concatenate energy files?


>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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-- 
Thanks,
J. N.
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